I hit 50 on my SI a few days ago and now I have been doing the HM's and working my way up the gear ladders.
In response to the OP, I believe that sure - some of the things your groups would have done are wrong, but with almost all 50's on HM's (including myself) are always going to skip conversations. So if you want them to the EM of the Flashpoint or Story Mode as that is made for story of course.
To your combat problem, it appears you are DPS and so I understand that. You have to understand that people don't want FP's to take very long anymore, and bonus missions are irrelevant because there is now no more xp gain (until Sunday) so if there is a way to get around fights people know about them and use them, if you are new to HM then you best hop on your speeder and follow suit - AND it saves time.
Your group probably just thought you had done the FP's before as many have and so they would not come back to help you.
I have not shared yet my combat aggro or whatever, but since this is my first 50 and I am a healer, I don't usually get complaints about drawing enemies because all the groups I have been in have supported me and if we have had several groups we have (just) pulled through.
The only real advice I can say is to play it like most play it to make the experience more fun for everyone.
Hope that helps